3B7P | pdb_00003b7p

Crystal structure of spermidine synthase from Plasmodium falciparum in complex with spermine

• PDB DOI: https://doi.org/10.2210/pdb3B7P/pdb

• Classification: TRANSFERASE
• Organism(s): Plasmodium falciparum 3D7
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-10-31 Released: 2007-11-20 
• Deposition Author(s): Qiu, W., Dong, A., Ren, H., Wu, H., Zhao, Y., Schapira, M., Wasney, G., Vedadi, M., Lew, J., Kozieradzki, I., Edwards, A.M., Arrowsmith, C.H., Weigelt, J., Sundstrom, M., Plotnikov, A.N., Bochkarev, A., Hui, R., Structural Genomics Consortium (SGC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.250 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of spermidine synthase from Plasmodium falciparum in complex with spermine.

Qiu, W., Dong, A., Ren, H., Wu, H., Zhao, Y., Schapira, M., Wasney, G., Vedadi, M., Lew, J., Kozieradzki, I., Edwards, A.M., Arrowsmith, C.H., Weigelt, J., Sundstrom, M., Plotnikov, A.N., Bochkarev, A., Hui, R.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 98.16 kDa 
• Atom Count: 7,491 
• Modeled Residue Count: 842 
• Deposited Residue Count: 849 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spermidine synthase	A, B, C	283	Plasmodium falciparum 3D7	Mutation(s): 0  Gene Names: PF11_0301 EC: 2.5.1.16
UniProt
Find proteins for Q8II73 (Plasmodium falciparum (isolate 3D7)) Explore Q8II73  Go to UniProtKB:  Q8II73

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MTA	E [auth A], G [auth B], I [auth C]	5'-DEOXY-5'-METHYLTHIOADENOSINE C11 H15 N5 O3 S WUUGFSXJNOTRMR-IOSLPCCCSA-N
SPM	D [auth A], F [auth B], H [auth C]	SPERMINE C10 H26 N4 PFNFFQXMRSDOHW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.250 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 199.483	α = 90
b = 134.584	β = 96.36
c = 48.37	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASES	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-11-20 
Deposition Author(s): Qiu, W., Dong, A., Ren, H., Wu, H., Zhao, Y., Schapira, M., Wasney, G., Vedadi, M., Lew, J., Kozieradzki, I., Edwards, A.M., Arrowsmith, C.H., Weigelt, J., Sundstrom, M., Plotnikov, A.N., Bochkarev, A., Hui, R., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2007-11-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description